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The crystal structure of an endo-beta-1,3-glucanase from alkaliphilic Nocardiopsis sp.strain F96
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 293 0.1M Tris-HCl pH 8.0, 1.3-1.4M Ammonium sulfate, 1% Ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.82 31.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.589 α = 90 b = 71.843 β = 90.21 c = 39.666 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 rhodium-coated mirror 2004-11-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.9 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.3 50 99.3 0.064 14.2 6.2 47558
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.35 95.7 0.35 4.8 4574
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.3 39.65 47531 2405 99.08 0.144 0.144 0.143 0.1619 0.162 0.1757 RANDOM 9.249
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.19 -0.27 -0.55 0.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_dihedral_angle_4_deg 19.269 r_dihedral_angle_3_deg 10.327 r_dihedral_angle_1_deg 7.084 r_sphericity_free 2.909 r_scangle_it 1.804 r_scbond_it 1.337 r_angle_refined_deg 1.25 r_sphericity_bonded 1.154 r_mcangle_it 0.921
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.867 r_dihedral_angle_4_deg 19.269 r_dihedral_angle_3_deg 10.327 r_dihedral_angle_1_deg 7.084 r_sphericity_free 2.909 r_scangle_it 1.804 r_scbond_it 1.337 r_angle_refined_deg 1.25 r_sphericity_bonded 1.154 r_mcangle_it 0.921 r_rigid_bond_restr 0.759 r_mcbond_it 0.627 r_nbtor_refined 0.309 r_nbd_refined 0.184 r_symmetry_vdw_refined 0.133 r_symmetry_hbond_refined 0.119 r_xyhbond_nbd_refined 0.086 r_chiral_restr 0.084 r_metal_ion_refined 0.072 r_bond_refined_d 0.007 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1859 Nucleic Acid Atoms Solvent Atoms 217 Heterogen Atoms 30
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection